GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PLT5 in Bacteroides faecis MAJ27

Align Polyol (xylitol):H+ symporter, PLT4 (characterized)
to candidate WP_010537714.1 KCY_RS0114120 MFS transporter

Query= TCDB::Q1XF07
         (519 letters)



>NCBI__GCF_000226135.1:WP_010537714.1
          Length = 309

 Score =  139 bits (350), Expect = 1e-37
 Identities = 96/320 (30%), Positives = 157/320 (49%), Gaps = 34/320 (10%)

Query: 32  YAFACAMLASMTSILLGYDIGVMSGAAIYIKRDLKVSDVKIEILLGIINLYSLIGSGLAG 91
           Y    +++A++   L GYD  V+SG    + +  ++  ++    +G   + S++G   AG
Sbjct: 9   YLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGSIVGVLFAG 68

Query: 92  RTSDWIGRRYTIVFAGAIFFVGALLMGFSPNYWFLMFGRFIAGIGIGYALMIAPVYTAEV 151
             SD +GR+ T+V +  +F   AL    S ++  L+  R I G+GIG   +++P+Y +EV
Sbjct: 69  ILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIVSPLYISEV 128

Query: 152 SPASSRGFLTSFPEVFINGGILLGYISNFA---------------FSKLSLKVGWRMMLG 196
           S A  RG L S  ++ +  G L  Y+ N+                 +K+ +   WR MLG
Sbjct: 129 SVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVTEVWRGMLG 188

Query: 197 VGALPSVILGVGVLAMPESPRWLVMRGRLGDAIKVLNKTSDSPEEAQLRLADIKRAAGIP 256
           +  LP+V+  + +  +PESPRWL+++G+   A+ +L K  +S  EA  +L +        
Sbjct: 189 MEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNE-------- 240

Query: 257 ESCTDDVVEVSKRSTGEGVWKELFLYPTPAIRHIVIAALGIHFFQQASGIDAVVLYSPTI 316
              T  V+    +S       E  L   P I   VI  + I    Q  G++AV+ Y P+I
Sbjct: 241 ---TKSVLTSETKS-------EWALLMKPGIFKAVIIGVCIAILGQFMGVNAVLYYGPSI 290

Query: 317 FEKAGIKSDTDKLLATVAVG 336
           FE AG+ S  D L   V VG
Sbjct: 291 FENAGL-SGGDSLFYQVLVG 309


Lambda     K      H
   0.323    0.140    0.414 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 389
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 519
Length of database: 309
Length adjustment: 31
Effective length of query: 488
Effective length of database: 278
Effective search space:   135664
Effective search space used:   135664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory